Basic wrangling reminders

Refresh some skills for data wrangling & summary statistics using functions in the dplyr package

Find the top 5 highest observations of trees by legal_status. Do some wrangling, make a graph.

top_5_status <- sf_trees %>% 
  count(legal_status) %>% #count function is recognizing groups, finding counts, and puts it in a nice table (takes group by, summarise, n and uses all of it). Can have multiple levels of grouping as well. 
drop_na(legal_status) %>% #removes missing values; careful when doing this bc can be problematic.
rename(tree_count = n) %>%  # new name replaces old name
relocate(tree_count) %>% 
#allows you to move things around by class (character or class) or location, or columns) 
  slice_max(tree_count, n = 5)

Make a graph of those top 5 observations by legal status.

ggplot(data = top_5_status, aes(x = fct_reorder(legal_status, tree_count), y = tree_count))+
  geom_col()+
  labs(x = "Legal Status", y = "Tree Count")+
  coord_flip()+
  theme_minimal()

A few more data wrangling refresher examples

Only want to keep observations (rows) for Blackwood Acacia Trees

blackwood_acacia <- sf_trees %>% 
  filter(str_detect(species, "Blackwood Acacia")) %>% #filter to keep observations if within the species variable the string is detected where that stric is x. not looking for a complete exact match but only looking for an observation where that string shows up. 
select(legal_status, date, latitude, longitude)

ggplot(data = blackwood_acacia, aes( x = longitude, y = latitude))+
  geom_point()
## Warning: Removed 27 rows containing missing values (geom_point).

tidyr::seperate() and unite() functions

Useful for combining or seperating columns

sf_trees_sep <- sf_trees %>% 
  separate(species, into = c("spp_scientific", "spp_common"), sep = "::")

Example: tidyr::unite()

sf_trees_unite <- sf_trees %>% 
  unite("id_status", tree_id:legal_status, sep = "_cool!_")

###Make some actual Maps of blackwood acacia trees in SF

st_as_as() to convert latitude and longitude to spatial coordinates.

blackwood_acacia_sp <- blackwood_acacia %>% 
  drop_na(longitude, latitude) %>% 
  st_as_sf(coords = c("longitude", "latitude"))

st_crs(blackwood_acacia_sp) = 4326 #sets coordinate reference system 

#graph using geom_sf
ggplot(data = blackwood_acacia_sp) +
  geom_sf(color = "darkgreen")

###Read in SF roads shapefile

sf_map <- read_sf(here("data", "sf_map", "tl_2017_06075_roads.shp")) # read in spatial shapfile 

st_transform(sf_map, 4326) # data will have same coordinate reference system 
## Simple feature collection with 4087 features and 4 fields
## geometry type:  LINESTRING
## dimension:      XY
## bbox:           xmin: -122.5136 ymin: 37.70813 xmax: -122.3496 ymax: 37.83213
## geographic CRS: WGS 84
## # A tibble: 4,087 x 5
##    LINEARID   FULLNAME     RTTYP MTFCC                                  geometry
##  * <chr>      <chr>        <chr> <chr>                          <LINESTRING [°]>
##  1 110498938… Hwy 101 S O… M     S1400 (-122.4041 37.74842, -122.404 37.7483, -…
##  2 110498937… Hwy 101 N o… M     S1400 (-122.4744 37.80691, -122.4746 37.80684,…
##  3 110366022… Ludlow Aly … M     S1780 (-122.4596 37.73853, -122.4596 37.73845,…
##  4 110608181… Mission Bay… M     S1400 (-122.3946 37.77082, -122.3929 37.77092,…
##  5 110366689… 25th Ave N   M     S1400 (-122.4858 37.78953, -122.4855 37.78935,…
##  6 110368970… Willard N    M     S1400 (-122.457 37.77817, -122.457 37.77812, -…
##  7 110368970… 25th Ave N   M     S1400 (-122.4858 37.78953, -122.4858 37.78952,…
##  8 110498933… Avenue N     M     S1400 (-122.3643 37.81947, -122.3638 37.82064,…
##  9 110368970… 25th Ave N   M     S1400  (-122.4854 37.78983, -122.4858 37.78953)
## 10 110367749… Mission Bay… M     S1400 (-122.3865 37.77086, -122.3878 37.77076,…
## # … with 4,077 more rows
ggplot(data = sf_map)+
  geom_sf()

Combine blackwood acacia tree observations and SF roads map

ggplot()+
  geom_sf(data = sf_map, size = 0.1, color = "darkgray")+
  geom_sf(data = blackwood_acacia_sp, color = "red", size = 0.5)+
  theme_void()

now interactive map!!!

tmap_mode("view")
## tmap mode set to interactive viewing
tm_shape(blackwood_acacia_sp)+
  tm_dots()